ZEB1-mediated fibroblast polarization controls inflammation and sensitivity to immunotherapy in colorectal cancer.

The EMT-transcription factor ZEB1 is heterogeneously expressed in tumor cells and in cancer-associated fibroblasts (CAFs) in colorectal cancer (CRC). While ZEB1 in tumor cells regulates metastasis and therapy resistance, its role in CAFs is largely unknown. Combining fibroblast-specific Zeb1 deletion with immunocompetent mouse models of CRC, we observe that inflammation-driven tumorigenesis is accelerated, whereas invasion and metastasis in sporadic cancers are reduced. Single-cell transcriptomics, histological characterization, and in vitro modeling reveal a crucial role of ZEB1 in CAF polarization, promoting myofibroblastic features by restricting inflammatory activation. Zeb1 deficiency impairs collagen deposition and CAF barrier function but increases NFκB-mediated cytokine production, jointly promoting lymphocyte recruitment and immune checkpoint activation. Strikingly, the Zeb1-deficient CAF repertoire sensitizes to immune checkpoint inhibition, offering a therapeutic opportunity of targeting ZEB1 in CAFs and its usage as a prognostic biomarker. Collectively, we demonstrate that ZEB1-dependent plasticity of CAFs suppresses anti-tumor immunity and promotes metastasis.

Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing.

In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools have emerged to identify potential drug repurposing candidates. However, these tools often require complex installation and lack intuitive visual network mining capabilities. To tackle these challenges, we introduce Drugst.One, a platform that assists specialized computational medicine tools in becoming user-friendly, web-based utilities for drug repurposing. With just three lines of code, Drugst.One turns any systems biology software into an interactive web tool for modeling and analyzing complex protein-drug-disease networks. Demonstrating its broad adaptability, Drugst.One has been successfully integrated with 21 computational systems medicine tools. Available at https://drugst.one, Drugst.One has significant potential for streamlining the drug discovery process, allowing researchers to focus on essential aspects of pharmaceutical treatment research.

Cracking the black box of deep sequence-based protein-protein interaction prediction.

Identifying protein-protein interactions (PPIs) is crucial for deciphering biological pathways. Numerous prediction methods have been developed as cheap alternatives to biological experiments, reporting surprisingly high accuracy estimates. We systematically investigated how much reproducible deep learning models depend on data leakage, sequence similarities and node degree information, and compared them with basic machine learning models. We found that overlaps between training and test sets resulting from random splitting lead to strongly overestimated performances. In this setting, models learn solely from sequence similarities and node degrees. When data leakage is avoided by minimizing sequence similarities between training and test set, performances become random. Moreover, baseline models directly leveraging sequence similarity and network topology show good performances at a fraction of the computational cost. Thus, we advocate that any improvements should be reported relative to baseline methods in the future. Our findings suggest that predicting PPIs remains an unsolved task for proteins showing little sequence similarity to previously studied proteins, highlighting that further experimental research into the 'dark' protein interactome and better computational methods are needed.

Inference of differential gene regulatory networks using boosted differential trees.

Summary: Diseases can be caused by molecular perturbations that induce specific changes in regulatory interactions and their coordinated expression, also referred to as network rewiring. However, the detection of complex changes in regulatory connections remains a challenging task and would benefit from the development of novel nonparametric approaches. We develop a new ensemble method called BoostDiff (boosted differential regression trees) to infer a differential network discriminating between two conditions. BoostDiff builds an adaptively boosted (AdaBoost) ensemble of differential trees with respect to a target condition. To build the differential trees, we propose differential variance improvement as a novel splitting criterion. Variable importance measures derived from the resulting models are used to reflect changes in gene expression predictability and to build the output differential networks. BoostDiff outperforms existing differential network methods on simulated data evaluated in four different complexity settings. We then demonstrate the power of our approach when applied to real transcriptomics data in COVID-19, Crohn's disease, breast cancer, prostate adenocarcinoma, and stress response in Bacillus subtilis. BoostDiff identifies context-specific networks that are enriched with genes of known disease-relevant pathways and complements standard differential expression analyses. Availability and implementation: BoostDiff is available at https://github.com/scibiome/boostdiff_inference.

Quantitative effects of formulation and process parameters on the structure of food emulsions stabilized with an unrefined by-product powder: A statistical approach.

Apple pomace powder is a sustainable food ingredient, but its more complex composition compared to commonly purified ingredients could curb its valorization. This study assesses how physicochemical properties, formulation and process factors influence the physical properties of the emulsion. The two main objectives were to: 1) unravel the structuring and stabilizing mechanisms of such complex systems and 2) account for interactions between various parameters instead of studying them separately. Thirty-one experimental samples were formulated to produce a variety of microstructures with droplet diameters ranging from 28 to 105 µm, textures with viscosity ranging from 135 to 2,490 mPa.s at 50 s-1 and stabilities. Using multicriteria selection of effects revealed that the concentration of the powder and the size of solid particles are the main levers for tailoring the structure-function relationships of the emulsions. Solid particles play a key role in both structuring and stabilizing the emulsions. Process parameters have an impact on the emulsification step by modifying the adsorption rate of solid particles. In conclusion, modelling advanced our understanding of stabilizing mechanisms of the emulsions produced by apple pomace and will enable efficient knowledge transfer for industrial applications.

Lip color diversity: An intricate study.

BACKGROUND: Lip investigations and characterizations in the literature are less prevalent than for skin, particularly on the topic of color diversity. However, as the consumer demand increases for a nude lip makeup result, that is, shades close to the bare lip color, the identification and modification of lip color is essential for the cosmetic industry. OBJECTIVE: The objective was to highlight lip color diversity among three ethnicities (Caucasian, African and Hispanic), through the use of a spectral color measurement device especially adapted to the lip area, and to consider lip color ethnic specificities and overlaps. MATERIALS AND METHODS: The inferior natural lip color was measured with a full-face hyperspectral imaging system, SpectraFace (Newtone Technologies, Lyon, France), on 410 healthy women aged 19 to 68 (Caucasian French, Caucasian American, African American, and Hispanic American women). A hierarchical ascending classification, was deployed to determine clusters based on the lip colorimetric parameters along two strategies to identify the best statistical analysis to preserve the lip color diversity. RESULTS: Lip color is a continuous color space, with great intra-ethnic and inter-ethnic diversity, especially for African American women in terms of chroma and lightness. Among the two strategies of data analysis, our two-step statistical clustering analysis yielded 11 groups (i.e., 11 lip tones), revealing an accurate representation of the scope of diversity, but also of the overlaps. CONCLUSION: The 11 lip tones/colors could potentially serve as target shades for the development of a more diverse and inclusive range of lip cosmetics, such as nude lipsticks.

Network medicine-based epistasis detection in complex diseases: ready for quantum computing.

Most heritable diseases are polygenic. To comprehend the underlying genetic architecture, it is crucial to discover the clinically relevant epistatic interactions (EIs) between genomic single nucleotide polymorphisms (SNPs)1-3. Existing statistical computational methods for EI detection are mostly limited to pairs of SNPs due to the combinatorial explosion of higher-order EIs. With NeEDL (network-based epistasis detection via local search), we leverage network medicine to inform the selection of EIs that are an order of magnitude more statistically significant compared to existing tools and consist, on average, of five SNPs. We further show that this computationally demanding task can be substantially accelerated once quantum computing hardware becomes available. We apply NeEDL to eight different diseases and discover genes (affected by EIs of SNPs) that are partly known to affect the disease, additionally, these results are reproducible across independent cohorts. EIs for these eight diseases can be interactively explored in the Epistasis Disease Atlas (https://epistasis-disease-atlas.com). In summary, NeEDL is the first application that demonstrates the potential of seamlessly integrated quantum computing techniques to accelerate biomedical research. Our network medicine approach detects higher-order EIs with unprecedented statistical and biological evidence, yielding unique insights into polygenic diseases and providing a basis for the development of improved risk scores and combination therapies.

Demographic confounders distort inference of gene regulatory and gene co-expression networks in cancer.

Gene regulatory networks (GRNs) and gene co-expression networks (GCNs) allow genome-wide exploration of molecular regulation patterns in health and disease. The standard approach for obtaining GRNs and GCNs is to infer them from gene expression data, using computational network inference methods. However, since network inference methods are usually applied on aggregate data, distortion of the networks by demographic confounders might remain undetected, especially because gene expression patterns are known to vary between different demographic groups. In this paper, we present a computational framework to systematically evaluate the influence of demographic confounders on network inference from gene expression data. Our framework compares similarities between networks inferred for different demographic groups with similarity distributions obtained for random splits of the expression data. Moreover, it allows to quantify to which extent demographic groups are represented by networks inferred from the aggregate data in a confounder-agnostic way. We apply our framework to test four widely used GRN and GCN inference methods as to their robustness w. r. t. confounding by age, ethnicity and sex in cancer. Our findings based on more than $ {44000}$ inferred networks indicate that age and sex confounders play an important role in network inference for certain cancer types, emphasizing the importance of incorporating an assessment of the effect of demographic confounders into network inference workflows. Our framework is available as a Python package on GitHub: https://github.com/bionetslab/grn-confounders.

The specific DNA methylation landscape in focal cortical dysplasia ILAE type 3D.

Focal Cortical Dysplasia (FCD) is a frequent cause of drug-resistant focal epilepsy in children and young adults. The international FCD classifications of 2011 and 2022 have identified several clinico-pathological subtypes, either occurring isolated, i.e., FCD ILAE Type 1 or 2, or in association with a principal cortical lesion, i.e., FCD Type 3. Here, we addressed the DNA methylation signature of a previously described new subtype of FCD 3D occurring in the occipital lobe of very young children and microscopically defined by neuronal cell loss in cortical layer 4. We studied the DNA methylation profile using 850 K BeadChip arrays in a retrospective cohort of 104 patients with FCD 1 A, 2 A, 2B, 3D, TLE without FCD, and 16 postmortem specimens without neurological disorders as controls, operated in China or Germany. DNA was extracted from formalin-fixed paraffin-embedded tissue blocks with microscopically confirmed lesions, and DNA methylation profiles were bioinformatically analyzed with a recently developed deep learning algorithm. Our results revealed a distinct position of FCD 3D in the DNA methylation map of common FCD subtypes, also different from non-FCD epilepsy surgery controls or non-epileptic postmortem controls. Within the FCD 3D cohort, the DNA methylation signature separated three histopathology subtypes, i.e., glial scarring around porencephalic cysts, loss of layer 4, and Rasmussen encephalitis. Differential methylation in FCD 3D with loss of layer 4 mapped explicitly to biological pathways related to neurodegeneration, biogenesis of the extracellular matrix (ECM) components, axon guidance, and regulation of the actin cytoskeleton. Our data suggest that DNA methylation signatures in cortical malformations are not only of diagnostic value but also phenotypically relevant, providing the molecular underpinnings of structural and histopathological features associated with epilepsy. Further studies will be necessary to confirm these results and clarify their functional relevance and epileptogenic potential in these difficult-to-treat children.

Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing.

In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools have emerged to identify potential drug repurposing candidates. However, these tools often require complex installation and lack intuitive visual network mining capabilities. To tackle these challenges, we introduce Drugst.One, a platform that assists specialized computational medicine tools in becoming user-friendly, web-based utilities for drug repurposing. With just three lines of code, Drugst.One turns any systems biology software into an interactive web tool for modeling and analyzing complex protein-drug-disease networks. Demonstrating its broad adaptability, Drugst.One has been successfully integrated with 21 computational systems medicine tools. Available at https://drugst.one, Drugst.One has significant potential for streamlining the drug discovery process, allowing researchers to focus on essential aspects of pharmaceutical treatment research.

Online bias-aware disease module mining with ROBUST-Web.

SUMMARY: We present ROBUST-Web which implements our recently presented ROBUST disease module mining algorithm in a user-friendly web application. ROBUST-Web features seamless downstream disease module exploration via integrated gene set enrichment analysis, tissue expression annotation, and visualization of drug-protein and disease-gene links. Moreover, ROBUST-Web includes bias-aware edge costs for the underlying Steiner tree model as a new algorithmic feature, which allow to correct for study bias in protein-protein interaction networks and further improves the robustness of the computed modules. AVAILABILITY AND IMPLEMENTATION: Web application: https://robust-web.net. Source code of web application and Python package with new bias-aware edge costs: https://github.com/bionetslab/robust-web, https://github.com/bionetslab/robust_bias_aware.

Effect of perceptive enrichment on the efficiency of simulated contexts: Comparing virtual reality and immersive room settings.

This study was designed within the methodological framework of sensory and consumer sciences, where conventionally internal and external validity are approached separately (e.g. CLT vs HUT). Here is explored the added value of new immersive strategies, such as virtual reality, on their ability to achieve both: internal and external validity. This article presents a comparative study between different experimental setups, involving more than 270 consumers. Two different immersive setups were appraised, simulating the consumption episode 'eating a sandwich for lunch in a park': a context room (N = 57) and a VR environment (N = 55). We added two control conditions: a real park in summer (N = 56) and scenario-only in sensory booths (duplicated condition, N1 = 59, N2 = 52). A set of sandwiches were evaluated in a between-participants design, with one duplicated recipe for a reliability assessment. Participants evaluated samples on hedonic criteria and closed the experiment with a questionnaire measuring their level of immersion. After classification of the questionnaire variables, seven underlying dimensions were identified, with significant differences between conditions on the credibility of the environment and the scenario. As expected, with strong external validity, the simulated environments were more immersive than the conventional booth with scenario and less immersive than a real-life environment. Although the immersive conditions did not stand out from the other conditions on the product evaluation performance, all the conditions revealed a high level of internal validity. Mean scores and rankings of the products, participants' repeatability and discriminatory power remained comparable to the real park environment indices.

Lacking mechanistic disease definitions and corresponding association data hamper progress in network medicine and beyond.

A long-term objective of network medicine is to replace our current, mainly phenotype-based disease definitions by subtypes of health conditions corresponding to distinct pathomechanisms. For this, molecular and health data are modeled as networks and are mined for pathomechanisms. However, many such studies rely on large-scale disease association data where diseases are annotated using the very phenotype-based disease definitions the network medicine field aims to overcome. This raises the question to which extent the biases mechanistically inadequate disease annotations introduce in disease association data distort the results of studies which use such data for pathomechanism mining. We address this question using global- and local-scale analyses of networks constructed from disease association data of various types. Our results indicate that large-scale disease association data should be used with care for pathomechanism mining and that analyses of such data should be accompanied by close-up analyses of molecular data for well-characterized patient cohorts.

Cardiac Tamponade as Initial Presentation of Systemic Lupus Erythematosus in Third-Trimester Pregnancy.

BACKGROUND Systemic lupus erythematosus (SLE) is a common autoimmune disorder in women of childbearing age. It can present during pregnancy and may lead to poor maternal and fetal outcomes with a higher risk of preterm birth and pre-eclampsia. Women are at a higher risk of lupus flares during pregnancy, especially if undiagnosed or disease is poorly controlled. Cardiac tamponade is a rare complication of SLE and can be fatal. CASE REPORT A 21-year-old primigravida African-American female with a history of asthma presented with progressive pleuritic left shoulder pain. She had a recent history of sore throat, facial rash, and depressed mood after sun exposure. Work-up was strongly positive for antinuclear antigen, anti-smith, anti-smith/ribonucleoprotein, anti-chromatin, anti-SSA, anti-SSB, anti-dsDNA, and low C3. Echocardiogram showed hemodynamically stable cardiac tamponade. Patient also had proteinuria and hypertension attributed to pre-eclampsia. However, a renal biopsy confirmed lupus nephritis. The patient was treated with pericardiocentesis, prednisone, azathioprine, and hydroxychloroquine. There was significant clinical improvement with resolution of cardiac tamponade and improvement in renal function. CONCLUSIONS Cardiac tamponade is a rare and life-threatening manifestation of SLE. Prompt work-up and treatment with immunosuppressants and pericardiocentesis is needed to improve maternal and fetal outcomes. SLE patients are at a higher likelihood of exacerbations of the disease during pregnancy. It also important to rule out lupus nephritis in an SLE patient with pre-eclampsia. This report has shown the importance of accurate diagnosis of SLE in pregnancy and the appropriate management to ensure the best outcomes for the mother and fetus.

Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST.

As the development of new drugs reaches its physical and financial limits, drug repurposing has become more important than ever. For mechanistically grounded drug repurposing, it is crucial to uncover the disease mechanisms and to detect clusters of mechanistically related diseases. Various methods for computing candidate disease mechanisms and disease clusters exist. However, in the absence of ground truth, in silico validation is challenging. This constitutes a major hurdle toward the adoption of in silico prediction tools by experimentalists who are often hesitant to carry out wet-lab validations for predicted candidate mechanisms without clearly quantified initial plausibility. To address this problem, we present DIGEST (in silico validation of disease and gene sets, clusterings or subnetworks), a Python-based validation tool available as a web interface (https://digest-validation.net), as a stand-alone package or over a REST API. DIGEST greatly facilitates in silico validation of gene and disease sets, clusterings or subnetworks via fully automated pipelines comprising disease and gene ID mapping, enrichment analysis, comparisons of shared genes and variants and background distribution estimation. Moreover, functionality is provided to automatically update the external databases used by the pipelines. DIGEST hence allows the user to assess the statistical significance of candidate mechanisms with regard to functional and genetic coherence and enables the computation of empirical $P$-values with just a few mouse clicks.